Analyzing microbial count data workshop
- John Calder
- 1 Course materials
- 2 Schedule Outline
- 3 Pre-workshop materials
Course materials
The course materials will be updated regularly on Bitbucket throughout the workshop. You can download the repository.
If you’re feeling git savvy, you can clone the repository.
If you’re not feeling git savvy but you want to, check out this fantastic free book: Happy Git and GitHub for the useR.
Schedule Outline
October 8 - Analyzing count data with regression modeling
From 1:20 - 4pm on Zoom
Regression models that predict microbial counts
Model based methods
Dirichlet Multinomial
Other model based approaches
Available tools
Range of regression packages and code
In house tools
What you’ll need to be ready for October 8
The R packages installed
The code and presentations are available on Bitbucket (see above for downloading)
Recording of workshop from October 8:
Password: gk$We4+?
October 6 - Analyzing count data for differential abundances
From 1 - 4pm on Zoom
Using the multinomial and Dirichlet distributions to model count data
Assessing differences in microbial proportions
Overview of Josh’s paper and tutorial of the R package CNVRG
What you’ll need to be ready for October 6
The R packages installed
The code and presentations are available on Bitbucket (see above for downloading)
Recording of workshop from October 6:
Password: =akb28kL
September 17 - Using the Bash shell with Teton
From 1:15 to 4pm on Zoom (we’ll start at 1:15 to make time for everyone to see the Botany seminar talks today)
Using the Bash shell on Windows, Mac, or Linux
Intro to using Teton
Working in an interactive session
Submitting jobs
What you’ll need to be ready for Thursday the 17th:
Access to Teton
See the Word document below under Pre-workshop materials for a guide to log on from Linda van Diepen
Please attempt to logon to Teton before we start this section on Thursday
If you cannot logon because you do not have a project associated with Teton fill out the form for a new project on your advisor’s behalf. Or if there is a project but you are not a user on that project, request that you be added to the current project.
Zoom
Run this html file in a browser to follow along
September 15 - Bioinformatics with DADA2
From 1 to 4pm on Zoom
Overview of raw reads, demultiplexing and splitting
For those in the EPSCoR Microbial Ecology Collaborative, please review https://microcollaborative.atlassian.net/wiki/spaces/MICLAB/pages/559055211
DADA2 tutorial with Gordon Custer
What you’ll need to be ready for Tuesday the 15th:
Zoom
Be sure you have the R Packages installed
email me with any problems (wcalder@uwyo.edu)
Download the R project from Bitbucket here (it’s the same link as above in the course materials). It’s a big one (> 1Gb), but it will make the first day easier
Recording from September 15:
Password: arNJ+rw6
Recording from September 17:
Unfortunately I forgot to press record for the middle of the workshop. I’m sorry - please ask me any questions about material I didn’t record.
Password: Gx$rh0i?
Pre-workshop materials
First time logging to Teton for windows users
Follow this document from Linda van Diepen if you use Windows and do not have a way to login to Teton yet
If you use MacOS or Linux, the bottom of the document shows you how to login in to Teton using the Terminal
